Sequence
atgc intronic sequence ATGC exonic sequencegtaggtttcatcttcttgaattcttaacttgtcagggttataagccaggccacattcttagcatttatcttttgcttgcagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g02120.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g02120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G000660_T01 (Zea mays), 3'ss of exon 3
----gtaggtttcatcttcttgaattcttaacttgtcagggttataagccaggccacattcttagcatttatcttttgcttgcagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC
|| | ||||| | || | || | | || | | | | | |||| | | || || | ||||||||| || |||||| |||| ||||| || | ||||||||||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||
gtaagtctgccccatctcatcatatgcgtagcactatgagatt-tgaaactgtttttttgcttatc--tatcctcttacacgcagCTTAACACGGCTTATCAGAAGCTAACCTCCATAAGGCCCTGTGGACCCAGCAAGAGAGCCATCCGCGCCGCAACCTATGATCTAGCTAAGAACGATCCAT
upper sequence: LOC_Os12g02120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G39890.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtaggtttcatcttcttgaattcttaacttgtcagggttataagccaggccacattctt---------agcatttatcttttgcttg--cagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC
| ||| || ||| || | | ||| || |||| || | | |||| ||| ||||| || ||| ||||| | |||||||| || || || |||||||| ||||| ||||| || |||| || ||||||||| | ||||||||||||||
gtgagtccgaaaccctcaccttgtcgttgaatccagaaacaatttccatactacttaatttttcacaagtgttatggttgaacatcatcaacttggtggtgaattggtgatagattggttcacagatttcttaattgagatttcattttttcacaaatgaatgtggcatttttctttggacagCTAAATGAAGCATATGATATGCTAACTTCAAAGAGACCTTGTGGACCAAATAAAAGAGCAATACGTGGCGCTACTTATGATTTGGCTAAGAATGATCCTT
upper sequence: LOC_Os12g02120.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G10940.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaggtttcatcttcttgaattcttaacttgtcagggttataagccaggccacattcttagcattt--atcttttgctt---gcagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC
||| |||| || ||| || |||| || | || || || || || || || | || || |||||||| || |||||||| | | || || | || ||||| || || || |||| ||||||| |||||| |||||||| ||||||||||||||
gtaagtttaatagtctca----ctctactt--caatccaagaaagtttcatactttttttgcgttctgattctgtgtttcgaacagCTTAACACGGCTTATGACACTTTGGTATCAAAGCGTCCATGTGGGCCTAACAAAGGAGCCATCCGTGGTGCAACATATGATCTGGCTAAGAATGATCCCTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29621076|gb|CB626087.1|CB626087EST: GAGCACCTGCAGTTGCAATTGCTTACATGTTTTGGTTCGAGAATATGAAT CTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAAT
genomic: GAGCACCTGCAGTTGCAATTGCTTACATGTTTTGGTTCGAGAATATGAATgtaggtttca ... ttgcttgcagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgtcagggttataagccaggccacattcttagcatttatcttttgcttgcagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC
tcttaac putative branch site (score: 2)
tttatcttttgctt putative PPT
atttatctttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtttcatcttcttgaattcttaacttgtcagggttataagccaggccacattcttagcatttatcttttgcttgcagCTTAAGACAGCTTATGAGAAACTAACTTCTAAAAGGCCCTGTGGACCCAATAAGAGAGCGATCCGTGCTGCAACTTATGATCTTGCTAAGAATGATCCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC